BioPortal Release Notes

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BioPortal Release 4.22.1 (December 2015)

Enhancements

  • Added configuration parameters at the UI layer that allow for a greater control over debugging issues with HTTP caching.

Bug Fixes

  • Fixed a bug in the HTTP caching code that caused multiple identical requests to bypass the cache and trigger extraneous requests to the REST API. The bug fix resulted in a significant performance boost to both the front- and back-end services.

BioPortal Release 4.22 (November 2015)

Enhancements

  • New functionality at the REST API level in support of our collaboration with the CEDAR project:
    • Added the ability to search for, and retrieve all value sets.
    • Implemented search for value set items (example link).
    • Implemented search for ontology classes and value set items (example link).
    • Added the ability to exclude value set collections from search (example link).
    • Added the ability to search for value set values across all value sets in an ontology.
  • Ontologies are now sortable by creation date on the Admin page.
  • Clicking the Add Comment and/or Add Proposal buttons in the Notes sections for ontologies will navigate unauthenticated users to the login page.


Bug Fixes

  • Fixed an issue that caused Projects page load times in excess of 3 minutes.
  • Fixed an issue that caused the UI to go blank after selecting the root node of the CCO ontology.
  • Admin page: the ontologies table now refreshes after deleting an ontology.
  • Fixed an issue that caused a 404 error when trying to view the DINTO ontology.
  • Fixed an inconsistency in the metadata for the CHMO ontology that caused the parsing process to fail.


BioPortal Release 4.21 (October 2015)

Bug Fixes

  • Fixed an issue that caused class trees to reload every time a class was selected.
  • Fixed an issue with BioPortal's term selection widget that caused raw HTML to be displayed in search results.
  • Fixed a problem in the REST API that caused an internal server error when accessing nonexistent users. The API now correctly displays a 404 not found message.
  • Fixed a bug that prevented flat tree ontologies from displaying in BioPortal.
  • Fixed an issue that prevented the latest versions of the Gazetteer and Chemical Entities of Biological Interest ontologies from parsing.
  • Fixed a problem that prevented visualization from working with private ontologies (thanks go to Eric Verbeek for this).


BioPortal Release 4.20 (August 2015)

This release includes minor fixes from several previous releases.

  • Released a new version of the Ontology Recommender. This version is more flexible than the previous version and allows users to assign weights to the scores for various factors that influence the recommendation. In addition, some edge cases in the old system that resulted in bad recommendations have been addressed. This new recommendation system was developed independently by Marcos Martinez and then incorporated into our base code.
  • Instances (individuals) in an ontology can now be accessed through the API. Documentation for this is available at: http://data.bioontology.org/documentation#Instance.
  • Components have been added to the Annotator UI to allow users to exercise additional options available through the API.
  • Icons now indicate non-subclass relationships in OBO ontologies. Previously it was not possible to distinguish visually OBO subclass from other OBO relations displayed in the tree (such as OBO part-of).
  • The UMLS MeSH vocabulary is now displayed hierarchically. Previously it was displayed as a flat list of terms because of some problems with the hierarchical relation in the source that we were using.
  • The Search API now allows search-by-name of provisional classes assigned to an ontology.
  • The UMLS ontologies have all been updated to the latest 2015AA release.
  • A new version of BioMixer with a simpler user interface has been incorporated into the system. This work was done by our collaborators at the University of Victoria.
  • Created both a REST service and a UI for BioPortal application administration. This interface is automatically visible to VM administrators.
  • Updated the framework of our system from RAILS version 2 to version 4.
  • Fixed many bugs, especially those causing failures when parsing an ontology.


BioPortal Release 4.14 (February 2015)

This release includes minor fixes from several previous releases.

  • The ontology summary page for each ontology now has a graph of recent history of the level of user-interface (UI) web traffic (number of page views) for that ontology. This graph is available under the “Metrics” box. See, for example, http://bioportal.bioontology.org/ontologies/SNOMEDCT . The raw data is also available for download in CSV format from the same location.
  • The BioPortal home page now has a link that displays all ontologies in the system and the number of UI views for each ontology. Previously usage of only the top 5 ontologies were available.
  • Users of our virtual machine now have the ability to plug in alternate concept recognizers for use by the annotator. To support these custom annotators, arbitrary parameters can be passed via the rest interface to the underlying concept recognizer. Documentation for how to make use of this feature is available on GitHub. Previously the “mgrep” concept recognizer was hardwired into the system and code modifications were required to employ another recognizer.
  • Ontologies views can now be used for annotation. Previously only top level ontologies were available for use by the annotation system.
  • All of PubMed has been indexed for use by the Resource Index for all terms in all ontologies in BioPortal. Previously only 18 months of PubMed data was indexed.
  • We now provide for download, for all resources in BioPortal, files containing counts for term occurrence and co-occurrence (occurrence of pairs of terms in a document). These files can be used for research in enrichment analysis. Documentation of the files and how they might be used is available on GitHub.
  • The ontology browse page now has a faceted interface that allows the list of displayed ontologies to be narrowed as desired. Previously all ontologies appeared in an alphabetical list but this became unwieldy with the 400+ ontologies that we now have.
  • There is now a user-interface for displaying all of the properties in an ontology. If the properties were created in a hierarchy then this hierarchy is displayed. Previously only the class hierarchy was displayed. Properties were available programmatically though the REST interface but this information was not surfaced in the UI.
  • Ontologies defined using SKOS are now supported. For these ontologies, the hierarchy is determined by the SKOS “broader” and “narrower” properties.
  • We now allow download of all publically available ontologies in RDF. UMLS ontologies with restrictive licenses are excluded.
  • We fixed a number of non-parsing ontologies and removed a bunch of low-content (“test”) ontologies.
  • The system now contains the latest versions (2014AB) of all UMLS ontologies.
  • We now treat all OBO synonym types as a BioPortal synonyms. Previously only the OBO “exact” synonym type was treated as a BioPortal synonym.
  • We now notify by email the ontology authors if the nightly pull of their ontology fails.


BioPortal Release 4.10 (September 2014)

This release includes minor fixes from several previous releases.

  • Reengineered the entire Resource Index to achieve better and more consistent performance and to align the Resource Index with the new BioPortal backend (released last year). In addition to allowing us to support additional resources, this revision removes a number of inconsistencies that resulted from the Resource Index using the old BioPortal backend.
  • Upgraded the OWL and OBO parser to the latest version and reparsed all OBO and OWL ontologies. This reprocessing fixed a large number of problems with ontologies that either did not parse or that failed search indexing or metrics calculations.
  • We now create and make available for download a comma-separated value (CSV) file for most ontologies. These files have one row/class and a standard set of properties in the columns. We cannot make these files available for ontologies if the license for the ontology does not permit it (e.g. SNOMED-CT and MedDRA).
  • Fixed PURLS for all ontologies. There were a large number of ontologies for which the PURLs we created, in the old system or the new one, no longer worked correctly.
  • Reworked the entire mappings system so that mappings will be always up-to-date with the latest version of the ontologies.
  • Created a web page (http://bioportal.bioontology.org/validate_ontology_file) so that users can validate that their ontologies parse correctly with the latest version of the OWL/OBO parser.
  • Removed a number of bogus ontologies and spam notes.
  • Fixed implementation of “longest only” parameter in Annotator.
  • We now reparse and reindex an ontology if the administrator of the ontology changes the metadata for the ontology. The reparse is necessary because the metadata contains information, such as the properties that contain synonyms or definitions, that influence the parsing and indexing.
  • Recalculated metrics for all ontologies. This process filled in metrics for many ontologies that lacked them, and corrected the calculations of some metrics in other ontologies.
  • We now allow the download of RDF (Turtle) files for UMLS ontologies whose license allows users to download them.
  • Reindexing ontologies for search no longer interferes with the use of search on those ontologies. Previously search for an ontology was either broken or incomplete for an ontology that was being indexed.
  • Added an ontology properties endpoint to the REST API. This endpoint allows a user to query for the properties used by an ontology.

As previously noted, we have permanently retired the old NCBO BioPortal API. New API documentation is available at http://data.bioontology.org/documentation.


BioPortal Release 4.6 (May 2014)

  • Improved Search Result Display – Many ontologies contain classes that are references to a canonical ontology that “owns” the class. The system now automatically tries to identify the “owning” ontology and emphasize it in the results while displaying the ontologies that contain references to that ontology as subordinate (for that class). This feature is easier to try out than to explain. Type in “cancer” into the search box on the Search Tab and scan through the results to see what it is all about. This sort of display has been requested by a number of users for quite a while and we are happy to finally provide it.
  • Implemented Search for ID (URI), UMLS CUI, UMLS TUI, and skos:notation – The search system now will use the input search to find a class URI, a class skos:notation field (“short id” in the old system) or a UMLS “concept unique identifier” or semantic type. All of these fields are available through the default search mechanism. There is still an optional “all properties” parameter to search these property values along with all other property values.
  • Released New Version of BioMixer visualization system – The BioMixer system has been updated to improve performance and be more robust. (Work performed by our University of Victoria collaborators.)
  • Implemented New Mapping Visualization – Mappings system now allows a user to visualize the strength of mappings relationships between ontologies. Go to the mappings tab, select an ontology, and hit the visualization radio button to try this out. (Work performed by our University of Victoria collaborators.)
  • Implemented Configurable REST API calls – The Annotator and Search REST calls now allow a user specify which fields of a class the system should return. The user can also specify “all” to get everything.
  • Updated UMLS Ontologies – All UMLS ontologies have been updated to the latest (2013 AB) version.
  • Improved Autocomplete – The autocomplete in the ontology “Jump To” box, and in the widgets, now works more reliably with results that are more intuitive than previously.
  • Provide Access Control for Mappings – We have implemented access control to prevent people other than the author from deleting a mapping.
  • Reimplemented Annotator “Longest Only” Parameter – We have reimplemented the annotator “longest only” parameter to work in all situations. This parameter allows the user to limit the returned results to only those matches which are longer than other matches for a given ontology. In the old system this parameter did not work correctly.
  • Reimplemented Widgets to not use Flash – We have reimplemented the widgets to not use the Adobe Flash technology. Requiring the use of this technology was unpopular among our user community.
  • Enabled Upload and Download Large Ontologies – We have fixed various timeout problems which prevented users from uploading or downloading large ontologies.
  • Fixed Bugs! – Fixed a very large number of bugs, some new with the new system, and some carried forward from the old system.


We've shut down access to the old BioPortal REST API and will be turning off the old system entirely in the near future. We've provided 7 months for application developers to move to the new system and the vast majority have already done so. The overwhelming response from developers has been the that new system is now (after a few post release glitches!) much easier to use and much more reliable than the old system. Documentation for the new API is available at: http://data.bioontology.org/documentation.


BioPortal Release 4.0 (September 2013)

The primary distinguishing feature of this release is the replacement of several backend storage and caching mechanisms with a single triple-store based backend built with on the open source 4store platform. In addition we are simultaneously releasing a new version of the BioPortal REST API. This API is also built on top of the triple store. It provides a much more uniform and REST-full interface to the underlying BioPortal data than our previous REST API.

The old API will continue to function through the end of 2013. This API will only be able to access “old content” (that is, ontologies submitted or updated before today). We encourage API users to transition as quickly as possible to the new API. The new API is the only way to access both new content (submitted after today) and old content. The reports from beta users of the new API have been uniformly positive. Draft documentation for the new API is available at http://data.bioontology.org/documentation

BioPortal users will note a few changes from the previous version. Some of these changes are temporary (we didn’t quite get everything done…) while others are permanent. There are also a number of minor and cosmetic changes. The list of the more important changes is available below.

With a release of this size, it is inevitable that some bugs have crept in. Please report any that you run across to the support@bioontology.org mailing list. Have confidence that we will be working diligently to prioritize and fix the problems that arise.

Temporary Changes

  • All handling of obsolete classes in UI and API is not supported yet. Obsolete classes are currently indistinguishable from normal classes.
  • “Slices” and ontology sets (user defined lists of ontologies of interest) are not supported yet
  • The tree browse UI does not yet distinguish between is-a and part-of relations for OBO ontologies. Previously (and probably in the future) icons next to the class name indicated the relationship type.
  • We do not yet have a VM version for this release. We expect to produce a new VM version by the end of the year. This VM will include the triple-store based storage mechanism. In addition VM users will be able to query the VM triple-store directly with SPARQL.
  • Parsing of new ontologies and new versions remains disabled for the next few days. We will re-enable parsing by early next week.

Permanent Additions

  • New ontologies and new versions of ontologies will be typically available for text annotation the next day after submission. Previously the process took several weeks to several months.
  • We now have the latest versions UMLS ontologies. Previously we updated UMLS ontologies on request only, which left us with some very old versions. Going forward we will try to update our set of UMLS ontologies within a month of the UMLS release.

Permanent Subtractions

  • Programmatic and browse access to classes in non-current versions of ontologies is removed. We still retain metadata about older versions of ontologies and we still allow you to download the source files for old versions.
  • We no longer support Protégé Frames format ontologies. Owners of these ontologies will need to convert them to OWL or OBO to load them.
  • We now use the owlAPI (http://owlapi.sourceforge.net/) to load OWL and OBO ontologies. This API supports OWL version 2.0. For almost all features, OWL 2.0 is a superset of OWL 1.0. There are some edge cases though where ontologies that marginally parsed with an OWL 1.0 parser will not parse at all with the OWL 2.0 parser. We leave it to OWL ontology owners to provide valid OWL 2.0 ontologies.


BioPortal Release 3.12

  • Implemented the display of the OBO part-of relationship in the term neighborhood visualization.
  • Improved some default layouts in the visualization system.
  • Updated automated mappings for all ontologies.
  • Regenerated the annotator hierarchy database. The versions of ontologies in this database are now much more current.
  • Implemented support for federated queries in the BioPortal SPARQL endpoint.
  • Moved the mappings from the BioPortal endpoint into a separate public endpoint. This change allows us to update automated mappings more cleanly.
  • Added the following resources to the Resource Index. All of these resources are the results of our collaboration with the Neuroscience Information Framework (NIF) group.
    • NIF PubMed Health: Tests
    • NIF Drug Related Gene Database
    • NIF Gemma
    • NIF Integrated Disease View
  • Fixed “Maximum Depth” metric for a number of ontologies. Was incorrectly displaying “1” in some cases.
  • Fixed web service failure when attempting to retrieve all concepts from several ontologies.
  • Fixed annotator to return all ancestor terms. Was missing some ancestors for some ontologies.
  • Fixed Search to work correctly in MeSH.
  • Fixed problem with SPARQL query to BioPortal endpoint on queries that include ORDER and LIMIT clauses

(Release February 2013)


BioPortal Release 3.10

  • Revised UI for the Resource Index. This new UI supports the BioPortal slice mechanism. The new UI is also much faster than the previous one.
  • Updated ontologies available for use with the Annotator which includes newer ontologies and more recent versions of existing ontologies.
  • Fixed a longstanding bug in the Annotator that caused paths from a term to root nodes to occasionally be truncated.
  • Allow submission of Notes on ontology terms by anonymous users. Previously a user had to be logged in to submit a note.

(Release July 2012)


BioPortal Release 3.9

  • We have revised the search interface, both for specifying a search and in the format of the returned results. The new “advanced search” capability allows users to specify more clearly exactly what terms they would like to find. This capability also allows us to choose better (more commonly desired) defaults for the “basic search”. The returned search results are now grouped by ontology and the results are ranked so that terms from “better” ontologies are returned first. We also show definitions for terms that have them. In general this response format was inspired by the Google search response interface so we hope that it looks familiar. We are specifically soliciting feedback from users on this revision. Please send any comments to support@bioontology.org. *
  • We include the first version of the BioMixer visualization software (available through the “Visualize” links). This software replaces the older FlexViz system. There are a number of technology improvements (i.e. the removal of Flash technology) over the older system and the newer system is more powerful as well (i.e. you can now navigate mappings from the basic interface). More complete versions of BioMixer will be introduced in subsequent releases. Please provide any feedback you can on this new system. *
  • We have regenerated all automatically generated mappings in the system. These include lexical mappings, UMLS CUI mappings, identical identifier mappings, and OBO-xref mappings. We have also loaded mappings between selected UMLS ontologies as specified in the UMLS database (MRMAP).

* This item was requested via the User Support mailing list. Thank you for your comments and suggestions!

(Release June 2012)


BioPortal Release 3.8

  • We have regenerated all mappings based on UMLS CUIs. Thus terms in different UMLS ontologies which share the same CUI are now mapped to each other. The mapping created is of type skos:closeMatch. There are now 3,000,000 of these UMLS CUI mappings in the system.*
  • We have regenerated all mappings based on xrefs (OBO cross-reference) in OBO ontologies. A mapping is now generated when a term in an OBO ontology has an xref to a term in another ontology. The mapping created is of type skos:relatedMatch. There are 35,000 of these xref mappings in the system.*
  • We have regenerated all mappings based on terms which have identical unique identifiers (IRIs). A mapping is now generated when term in an ontology has a unique identifier that is identical to the identifier of a term in another ontology. The mapping created is of type skos:exactMatch. There are 700,000 of these identical IRI mappings in the system.*

We also fixed a number of bugs which were causing performance, stability, and ontology upload problems.

*This item was requested via the User Support mailing list and the NCBO User Group. Thank you for your comments and suggestions!

(Release May 2012)


BioPortal Release 3.7

  • Updated term mappings generated by LOOM
  • Added boolean functionality to Search Web service and UI
  • Updated ontology content for the Resource Index
  • BioPortal SPARQL endpoint beta release, http://sparql.bioontology.org
  • Modified response of Annotator UI to not fail if input text contains returns or results do not have any term matches*
  • Bug fix for Term Autocomplete widget to remove namespace collision with jQuery widgets*

* This item was requested via the User Support mailing list and the NCBO User Group. Thank you for your comments and suggestions!

(Release April 2012)


BioPortal Release 3.6

* This item was requested via the User Support mailing list and the NCBO User Group. Thank you for your comments and suggestions!

(Release January 2012)


BioPortal Release 3.5

  • Added ability for logged-in users to filter which ontologies appear in their BioPortal display
  • Updated Annotator page to simplify the selection of options, to clarify the annotation results, and to remove Flash from the implementation
  • Improved Annotator Web service response performance by 5-10x*
  • Added ability for the ontology Web services API to optionally return JSON (rather than XML)*
  • Updated Ontology Recommender algorithm to provide better recommendations*
  • Added display of matched terms for Ontology Recommender*
  • Added Web service to get all namespaces for an ontology*
  • Bug Fixes
    • Display user-friendly names for RxNorm ontology properties

* This item was requested via the User Support mailing list and the NCBO User Group. Thank you for your comments and suggestions!

(Release December 2011)


BioPortal Release 3.4

  • Revised the Term Mappings tab to ease the creation of term-to-term mappings*
  • Limited access to “Private” ontologies via the Browse and Search pages
  • Added backend support to allow multiple administrators for a single ontology*
  • Added ability to copy to the clipboard a permanent link to any BioPortal term*
  • Bug Fixes
    • Resolved issue causing search to not display all matching terms*
    • Fixed Term Mappings tab display for IE 7 & 8*
    • Fixed RDF Ontology Download Web service
    • Fixed link to the list of resources included in the Resource Index*

* This item was requested via the User Support mailing list and the NCBO User Group. Thank you for your comments and suggestions!

(Release October 2011)


BioPortal Release 3.3

New features include updates to the Web interface and Web services:

  • Added Get Properties Web service, http://www.bioontology.org/wiki/index.php/NCBO_REST_services#Property_Services
  • Updated Search page to remove Flash
  • Handling of obsolete terms, part 2 – term name is grayed out and <is_obsolete> element is returned in Web service response for obsolete terms from OWL ontologies.
  • Added Help documentation
  • Implemented a feature to allow ontology submitters to flag their ontology as “licensed”. This feature allows the ontology submitter to require users to provide license information before they are allowed to access the ontology.
  • Bug Fix
    • Fixed the Filter by Account on the Mappings tab

(Release date September 2011)


BioPortal Release 3.2

New features include updates to the Web interface and Web services:

  • Added Ontology Recommender feature, http://bioportal.bioontology.org/recommender
  • Added support for access control for viewing ontologies
  • Added link to subscribe to BioPortal Notes emails
  • Synchronized “Jump To” feature with ontology parsing and display
  • Added documentation on Ontology Groups
  • Annotator Web service – disabled use of “longest only” parameter when also selecting “ontologies to expand” parameter
  • Removed the metric "Number of classes without an author"
  • Handling of obsolete terms, part 1 – term name is grayed out and <is_obsolete> element is returned in Web service response for obsolete terms from OBO and RRF ontologies. This feature will be extended to cover OWL ontologies in a subsequent release.
  • Bug Fix
    • Fixed calculation of “Classes with no definition” metric
    • Added re-direct from old BioPortal URL format to new URL format to provide working links from archived search results


Firefox Extension for NCBO API Key: To make it easier to test Web service calls from your browser, we have released the NCBO API Key Firefox Extension. This extension will automatically add your API Key to NCBO REST URLs any time you visit them in Firefox. The extension is available at Mozilla's Add-On site. To use the extension, follow the installation directions, restart Firefox, and add your API Key into the “Options” dialog menu on the Add-Ons management screen. After that, the extension will automatically append your stored API Key any time you visit http://rest.bioontology.org.

Upcoming software license change: The next release of NCBO software will be under the two-clause BSD license rather than under the currently used three-clause BSD license. This change should not affect anyone’s use of NCBO software and this change is to a less restrictive license. More information about these licenses is available at the site: http://www.opensource.org/licenses. Please contact support@bioontology.org with any questions concerning this change.


BioPortal Release 3.1

New features include updates to the Web interface and Web services:

  • Support for loading OWL 2 ontologies
  • Security Framework, part 2 - The apikey parameter is now required for all Web services. Login to BioPortal to get your API Key.
  • Browsing of ontologies that contain large numbers of sibling terms
  • Icons for is_a and part_of are displayed for OBO format ontologies
  • Display of the “occurs_in” relationship used in the Extended version of the Gene Ontology

Bug Fix

  • Added informative error message when incompatible parameter values are used in the Annotator Web service and updated Perl client to capture this error response

(Release date July 8, 2011)


BioPortal Release 3.0

New features include updates to the Web interface and Web services:

  • Web interface updates
  • Browse page now displays ontology features, e.g. size of the ontology, number of notes added to the ontology, number of projects that use the ontology, and number of reviews of the ontology
  • New ontology summary details page highlights the ontology metrics, reviews, projects, and derived views of the ontology
  • Security Framework, part 1 - Added apikey parameter to all Web services. The apikey parameter is optional until June 15, 2011, after this time the apikey parameter will be required for usage of the Web services. Login to BioPortal to get your API key.
  • Provisional Term Web service - New term proposals now receive a provisional term id. Additional Web services are now available for submitting provisional terms. For more details, see: http://www.bioontology.org/wiki/index.php/BioPortal_Provisional_Terms
  • Form auto-complete Widget - Option to include term definition in display
  • Resource Index
    • Data indexed with new ontologies from BioPortal
    • PubMed data now available for abstracts published in 2010

(Release date May 19, 2011)


BioPortal Release 2.6.4

New features include additional Web services and Web interface enhancements:

(Release date February 2011)


BioPortal Release 2.5

New features in this release include the following:

  • Support for structured notes and term requests: Users can now use BioPortal to request that content developers add new terms or update other ontology content. BioPortal provides a structured template for making such requests, allowing users to suggest preferred names, synonyms, and definitions for the requested terms. BioPortal stores the requests as structured notes that are attached to the ontology and that other ontology tools, such as Protégé, will be able to use.
  • Support for email notifications to interested parties whenever a BioPortal user creates new notes for an ontology of interest. (If you would like to subscribe to notifications about a particular ontology, please send email to support at bioontology.org. We will have an interactive form to sign-up for notifications shortly.)
  • Prototype Web services to generate RDF representation for terms in ontologies in BioPortal (see documentation [1] for details).
  • Web services for retrieving instance information for OWL ontologies [1]. We are planning to release a user interface for viewing instances shortly.
  • New ontology widgets that developers can embed on their Web sites, including an ontology tree widget that allows Web-site authors to present a display of an ontology or an ontology subtree for any BioPortal ontology in any Web page.
  • Preview release of Bio-Mixer, a mashup tool that provides extremely flexible browsing and exploration of ontologies and their mappings

[1] http://www.bioontology.org/wiki/index.php/NCBO_REST_services

(Release date June 9, 2010)

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